From 8519e12a474ec5337036136e19c66ed9352ac91a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 1 Dec 2016 10:31:00 +0100 Subject: [PATCH 1/6] change conda channel order --- config/galaxy.ini.sample | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index a50baf8afb71..255d1ac6bda3 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -203,7 +203,8 @@ paste.app_factory = galaxy.web.buildapp:app_factory # Pass debug flag to conda commands. #conda_debug = False # conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html) -#conda_ensure_channels = conda-forge,r,bioconda,iuc +# the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8) +#conda_ensure_channels = bioconda,r,defaults,conda-forge,iuc # Set to True to instruct Galaxy to look for and install missing tool # dependencies before each job runs. #conda_auto_install = False From 1f221aab22f4840d18847859f5099d4dc721b864 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 1 Dec 2016 10:35:01 +0100 Subject: [PATCH 2/6] change channel order --- lib/galaxy/tools/deps/resolvers/conda.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index a21a37ebd4a9..adcdc180661e 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -31,7 +31,7 @@ DEFAULT_BASE_PATH_DIRECTORY = "_conda" DEFAULT_CONDARC_OVERRIDE = "_condarc" -DEFAULT_ENSURE_CHANNELS = "conda-forge,r,bioconda,iuc" +DEFAULT_ENSURE_CHANNELS = "bioconda,r,defaults,conda-forge,iuc" log = logging.getLogger(__name__) From 0c91f65a99c43608faaa9f7b504646a326d6adaa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 1 Dec 2016 10:37:17 +0100 Subject: [PATCH 3/6] Change channel order in documentation --- doc/source/admin/dependency_resolvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index 6ec8e9f6804d..b463518b925f 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -182,7 +182,7 @@ debug ensure_channels conda channels to enable by default. See http://conda.pydata.org/docs/custom-channels.html for more - information about channels. (default: conda-forge,r,bioconda,iuc). + information about channels. (default: bioconda,r,defaults,conda-forge,iuc). auto_install Set to True to instruct Galaxy to look for and install missing tool From 8a80b2dc712bd16465197799a4ef3cc8dab01bc9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 12 Dec 2016 21:28:10 +0100 Subject: [PATCH 4/6] change order in galaxy.ini --- config/galaxy.ini.sample | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 255d1ac6bda3..e334c9357a06 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -204,7 +204,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory #conda_debug = False # conda channels to enable by default (http://conda.pydata.org/docs/custom-channels.html) # the recommended channel order is the one from BioConda (https://github.com/bioconda/bioconda-recipes/blob/master/config.yml#L8) -#conda_ensure_channels = bioconda,r,defaults,conda-forge,iuc +#conda_ensure_channels = iuc,bioconda,r,defaults,conda-forge # Set to True to instruct Galaxy to look for and install missing tool # dependencies before each job runs. #conda_auto_install = False From 3d492657028b3a29c9e3707cb609db87f4a783f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 12 Dec 2016 21:28:49 +0100 Subject: [PATCH 5/6] change oder in docs --- doc/source/admin/dependency_resolvers.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/admin/dependency_resolvers.rst b/doc/source/admin/dependency_resolvers.rst index b463518b925f..56453540bfc4 100644 --- a/doc/source/admin/dependency_resolvers.rst +++ b/doc/source/admin/dependency_resolvers.rst @@ -182,7 +182,7 @@ debug ensure_channels conda channels to enable by default. See http://conda.pydata.org/docs/custom-channels.html for more - information about channels. (default: bioconda,r,defaults,conda-forge,iuc). + information about channels. (default: iuc,bioconda,r,defaults,conda-forge). auto_install Set to True to instruct Galaxy to look for and install missing tool From f693643ea87dc807277cb6c2e8c3a2f9946fe5d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 12 Dec 2016 21:29:23 +0100 Subject: [PATCH 6/6] change channel order in conda.py --- lib/galaxy/tools/deps/resolvers/conda.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py index adcdc180661e..b39185d1b84a 100644 --- a/lib/galaxy/tools/deps/resolvers/conda.py +++ b/lib/galaxy/tools/deps/resolvers/conda.py @@ -31,7 +31,7 @@ DEFAULT_BASE_PATH_DIRECTORY = "_conda" DEFAULT_CONDARC_OVERRIDE = "_condarc" -DEFAULT_ENSURE_CHANNELS = "bioconda,r,defaults,conda-forge,iuc" +DEFAULT_ENSURE_CHANNELS = "iuc,bioconda,r,defaults,conda-forge" log = logging.getLogger(__name__)